[med-svn] [bwa] 02/02: Try to track down upstream issue #108 but no real progress - any help would be welcome

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit cb25d51d199ae51ae479588b96c73804e9b7ff48
Author: Andreas Tille <tille at debian.org>
Date:   Thu Mar 16 13:24:05 2017 +0100

    Try to track down upstream issue #108 but no real progress - any help would be welcome
---
 debian/changelog           |  8 ++++++++
 debian/patches/debug.patch | 13 ++++++++++---
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9f8d5fb..342b4f2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+bwa (0.7.15-4) UNRELEASED; urgency=medium
+
+  * Debugging (see deactivated patch debian/patches/debug.patch that tries
+    to track down upstream issue #108)
+    ==> Any help would be welcome!
+
+ -- Andreas Tille <tille at debian.org>  Thu, 16 Mar 2017 09:12:09 +0100
+
 bwa (0.7.15-3) unstable; urgency=medium
 
   * bwa/kseq.h is used by SeqLib so include this into libbwa-dev package
diff --git a/debian/patches/debug.patch b/debian/patches/debug.patch
index 032e94d..4cdb9e8 100644
--- a/debian/patches/debug.patch
+++ b/debian/patches/debug.patch
@@ -1,3 +1,10 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 16 Mar 2017 09:12:09 +0100
+Description: Try to address https://github.com/lh3/bwa/issues/108
+ BWA is crashing reproducibly on different computers in
+      seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
+ but at different states of data.  No idea what might be wrong here.
+
 --- a/bwtsw2_pair.c
 +++ b/bwtsw2_pair.c
 @@ -119,15 +119,19 @@ void bsw2_pair1(const bsw2opt_t *opt, in
@@ -5,19 +12,19 @@
  	if (end - beg < l_mseq) return;
  	// generate the sequence
 -	seq = malloc(l_mseq + (end - beg));
-+fprintf(stderr, "%s(%i): l_mseq = %i, end = %i, beg = %i, allocating %s\n", __FILE__, __LINE__, l_mseq, end, beg, l_mseq + (end - beg)); fflush( stderr );
++fprintf(stderr, "%s(%i): l_mseq = %i, end = %i, beg = %i, allocating %i\n", __FILE__, __LINE__, l_mseq, end, beg, l_mseq + (end - beg)); fflush( stderr );
 +	seq = malloc(l_mseq + (end - beg) + 1);
  	ref = seq + l_mseq;
  	for (k = beg; k < end; ++k)
  		ref[k - beg] = pac[k>>2] >> ((~k&3)<<1) & 0x3;
  	if (h->is_rev == 0) {
-+/* fprintf(stderr, "%s(%i): l_mseq = %i\n", __FILE__, __LINE__, l_mseq); fflush( stderr ); */
++fprintf(stderr, "%s(%i): l_mseq = %i\n", __FILE__, __LINE__, l_mseq); fflush( stderr );
  		for (i = 0; i < l_mseq; ++i) { // on the reverse strand
  			int c = nst_nt4_table[(int)mseq[i]];
 +fprintf(stderr, "%s(%i): i=%i, l_mseq = %i, c=%i, writing to position: l_mseq - 1 - i = %i\n", __FILE__, __LINE__, i, l_mseq, c, l_mseq - 1 - i); fflush( stderr );
  			seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
  		}
-+/* fprintf(stderr, "%s(%i): i = %i\n", __FILE__, __LINE__, i); fflush( stderr ); */
++fprintf(stderr, "%s(%i): i = %i\n", __FILE__, __LINE__, i); fflush( stderr );
  	} else {
  		for (i = 0; i < l_mseq; ++i) // on the forward strand
  			seq[i] = nst_nt4_table[(int)mseq[i]];

-- 
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